Variant 15-66387311-T-TC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_002755.4(MAP2K1):c.-31dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0954 in 1,516,248 control chromosomes in the GnomAD database, including 8,983 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 977 hom., cov: 31)

Exomes 𝑓: 0.095 ( 8006 hom. )

Consequence

MAP2K1
NM_002755.4 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.965

Variant links:

Genes affected

MAP2K1 (HGNC:6840): (mitogen-activated protein kinase kinase 1) The protein encoded by this gene is a member of the dual specificity protein kinase family, which acts as a mitogen-activated protein (MAP) kinase kinase. MAP kinases, also known as extracellular signal-regulated kinases (ERKs), act as an integration point for multiple biochemical signals. This protein kinase lies upstream of MAP kinases and stimulates the enzymatic activity of MAP kinases upon wide variety of extra- and intracellular signals. As an essential component of MAP kinase signal transduction pathway, this kinase is involved in many cellular processes such as proliferation, differentiation, transcription regulation and development. [provided by RefSeq, Jul 2008]

MAP2K1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 15-66387311-T-TC is Benign according to our data. Variant chr15-66387311-T-TC is described in ClinVar as [Benign]. Clinvar id is 40710.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAP2K1	NM_002755.4 linkuse as main transcript	c.-31dup		5_prime_UTR_variant	1/11	ENST00000307102.10
MAP2K1	XM_017022411.3 linkuse as main transcript	c.-31dup		5_prime_UTR_variant	1/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP2K1	ENST00000307102.10 linkuse as main transcript	c.-31dup		5_prime_UTR_variant	1/11	1	NM_002755.4	P1	Q02750-1

Frequencies

GnomAD3 genomes

AF:

0.102

AC:

15489

AN:

151718

Hom.:

978

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0940

Gnomad AMI

AF:

0.0463

Gnomad AMR

AF:

0.133

Gnomad ASJ

AF:

0.132

Gnomad EAS

AF:

0.337

Gnomad SAS

AF:

0.112

Gnomad FIN

AF:

0.0818

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.0836

Gnomad OTH

AF:

0.115

GnomAD3 exomes

AF:

0.119

AC:

18384

AN:

154242

Hom.:

1483

AF XY:

0.116

AC XY:

9435

AN XY:

81526

show subpopulations

Gnomad AFR exome

AF:

0.0905

Gnomad AMR exome

AF:

0.159

Gnomad ASJ exome

AF:

0.128

Gnomad EAS exome

AF:

0.334

Gnomad SAS exome

AF:

0.0961

Gnomad FIN exome

AF:

0.0807

Gnomad NFE exome

AF:

0.0832

Gnomad OTH exome

AF:

0.115

GnomAD4 exome

AF:

0.0947

AC:

129233

AN:

1364416

Hom.:

8006

Cov.:

AF XY:

0.0947

AC XY:

63904

AN XY:

675044

show subpopulations

Gnomad4 AFR exome

AF:

0.0910

Gnomad4 AMR exome

AF:

0.156

Gnomad4 ASJ exome

AF:

0.129

Gnomad4 EAS exome

AF:

0.369

Gnomad4 SAS exome

AF:

0.0964

Gnomad4 FIN exome

AF:

0.0832

Gnomad4 NFE exome

AF:

0.0824

Gnomad4 OTH exome

AF:

0.107

GnomAD4 genome

AF:

0.102

AC:

15484

AN:

151832

Hom.:

977

Cov.:

AF XY:

0.103

AC XY:

7636

AN XY:

74170

show subpopulations

Gnomad4 AFR

AF:

0.0938

Gnomad4 AMR

AF:

0.133

Gnomad4 ASJ

AF:

0.132

Gnomad4 EAS

AF:

0.337

Gnomad4 SAS

AF:

0.111

Gnomad4 FIN

AF:

0.0818

Gnomad4 NFE

AF:

0.0836

Gnomad4 OTH

AF:

0.115

Alfa

AF:

0.0935

Hom.:

136

Bravo

AF:

0.108

Asia WGS

AF:

0.205

AC:

709

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	Apr 15, 2014	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, no assertion criteria provided	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Oct 07, 2008	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over